I am getting an error comparing an Azure db to a local sql 2012 db that is empty. I've just done a successful compare and deployment with a different azure db and a different local sql 2012 db that was empty.

Can you try setting the SQL Compare project option "Ignore->Full-text indexing"? I think the text of the error message refers to a column name in the information schema that refers to a table containing fulltext indexes.

It looks like the SQL Compare code is treating the Azure database as if it were regular 2012, which has the index property "property_list_id" on full-text indexes. The source code indicates that it should gather this information on 2012 and ignore it on Azure... possibly SQL Compare is not detecting Azure correctly. Will have to look into that.

If it's any help, it looks like the live database in your error report is using SQL Server 2008 compatibility mode. I tried that in my test, but it did not reproduce the error. However, it may explain why you have this problem with some databases and not others. The bug that your error report got filed with mentions that it's a problem with SQL 2000 backward-compatibility.